303 commits

Author	SHA1	Message	Date
Alexander Peltzer	a6d08ed646	Adjust custom pipeline config for ampliseq on BINAC	2019-12-11 16:09:44 +01:00
Maxime Garcia	9497b78149	Merge pull request #100 from MaxUlysse/UPPMAX ... Improve UPPMAX configs	2019-12-06 10:52:44 +01:00
Maxime Garcia	79528de92f	Update docs/uppmax.md ... Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>	2019-12-06 10:47:09 +01:00
jfy133	1650080b6e	Linting	2019-12-05 17:03:07 +01:00
jfy133	731372dac2	Added SHH specific EAGER configuration	2019-12-05 17:01:10 +01:00
MaxUlysse	a63ec24626	Merge branch 'UPPMAX' of github.com:MaxUlysse/nf-core_configs into UPPMAX	2019-12-05 15:18:04 +01:00
MaxUlysse	99afe86ea9	update docs	2019-12-05 15:18:01 +01:00
Maxime Garcia	78826c9d4e	Merge branch 'master' into UPPMAX	2019-12-05 12:52:34 +01:00
Alexander Peltzer	9cdb915efb	Merge pull request #101 from jfy133/master ... Condensing SHH profile(s) with sub-profiles	2019-12-05 12:51:31 +01:00
jfy133	54dafbcfa3	Condensing SHH profiles following https://github.com/nf-core/configs/pull/100	2019-12-05 12:09:11 +01:00
MaxUlysse	cdbdbee0eb	replace -profile uppmax_devel by -profile uppmax,devel	2019-12-05 11:49:44 +01:00
Maxime Garcia	2669401a72	Merge branch 'master' into sarek	2019-11-27 13:27:43 +01:00
James A. Fellows Yates	c725c71e4d	Merge branch 'master' into master	2019-11-26 20:34:42 +01:00
jfy133	6f40c13473	Split shh config for each cluster	2019-11-26 20:20:17 +01:00
phue	672f025639	cbe: add documentation about iGenomes	2019-11-26 18:09:20 +01:00
Alexander Peltzer	81739a3907	Merge pull request #93 from jfy133/master ... Updated max resources for SHH SDAG	2019-11-26 15:56:39 +01:00
James A. Fellows Yates	89506a653c	Remove empty lines in block quotes for linting	2019-11-26 15:34:25 +01:00
James A. Fellows Yates	12ec22838c	Specified max sources currently at SDAG limits (exceeds cdag)	2019-11-26 15:29:03 +01:00
noirot	07b1f17d6a	correct md to pass linter	2019-11-26 15:02:06 +01:00
Noirot Céline	3ed206b7a7	Update docs/genotoul.md ... ok Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-11-26 14:52:45 +01:00
Noirot Céline	288294994e	Update docs/genotoul.md ... ok Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-11-26 14:52:32 +01:00
noirot	e95196451f	correct md to pass linter	2019-11-26 14:47:23 +01:00
noirot	42c949db95	correct md to pass linter	2019-11-26 14:43:42 +01:00
Alexander Peltzer	23f9fd2d73	Merge branch 'master' into master	2019-11-26 14:20:36 +01:00
Noirot Céline	42d99e7006	Update genotoul.md	2019-11-26 13:18:34 +01:00
Maxime Garcia	f6c2e4c65f	Update docs/pipeline/sarek/munin.md ... Update conf/pipeline/sarek/munin.config testing out module and containers collision	2019-11-26 11:57:51 +01:00
MaxUlysse	25d4e92935	update docs	2019-11-26 11:55:36 +01:00
Maxime Garcia	b029ccaa59	Update docs/pipeline/sarek/munin.md ... Update conf/pipeline/sarek/munin.config	2019-11-26 11:48:11 +01:00
MaxUlysse	283abcece4	update docs	2019-11-26 11:25:29 +01:00
MaxUlysse	cd1d0b5f8f	Add specific sarek config base, munin specific sarek config and docs ... rename file improve configs remove unnecessary params	2019-11-26 11:25:29 +01:00
Alexander Peltzer	aeb2fb6dc0	Fix all the markdownlinting errors	2019-11-26 00:48:17 +01:00
Noirot Céline	ed4436c1a6	Merge branch 'master' into master	2019-11-25 16:24:12 +01:00
noirot	db51c49b2f	Add genotoul config	2019-11-25 14:54:25 +01:00
MaxUlysse	08a6b74825	add new profile to be shared: awsbatch	2019-11-19 14:16:06 +01:00
Alexander Peltzer	d2603a134e	Add in denbi cloud configs	2019-11-11 12:26:19 +01:00
Phil Ewels	6790dbd4a3	Merge pull request #82 from arontommi/dev ... documentation on how to fix bianca "Requested node configuration is not available" problem	2019-11-08 15:07:07 +01:00
Phil Ewels	5e7d13df89	Update uppmax.md	2019-11-08 10:59:34 +01:00
arontommi	3f534c154e	documentation on how to fix bianca cluster configuration problem	2019-11-07 13:06:31 +01:00
arontommi	99f4d9b9bd	documentation on how to fix bianca cluster configuration problem	2019-11-06 13:10:09 +01:00
maxibor	47a7d57db4	update shh doc	2019-10-28 16:09:00 +01:00
phue	5a9dbe5d7c	MENDEL is no more ... the cluster is no longer operational, was replaced by CBE	2019-10-28 14:11:34 +01:00
Alexander Peltzer	5348b8c609	Revert "BINAC SMP / Short / Long Updates"	2019-10-28 13:12:31 +01:00
Alexander Peltzer	b5b2dd817f	Merge all	2019-10-27 13:24:45 +01:00
Anthony Bretaudeau	883a761651	add link	2019-10-16 18:45:26 +02:00
Anthony Bretaudeau	1f2786c78f	add genouest cluster	2019-10-16 18:15:04 +02:00
phue	9b3fda36f6	update singularity version ... singularity/3.1.0 is not available anymore	2019-10-10 21:22:19 +02:00
phue	5e257e7e9a	add cbe profile	2019-09-22 16:45:09 +02:00
MaxUlysse	f69524d59a	feat: update docs	2019-08-07 11:56:10 +02:00
MaxUlysse	332ba0dadb	fix: update and rearrange munin configuration file and docs	2019-08-07 11:10:48 +02:00
Martin Proks	c583aa0233	Added kraken config (#15) ... * Added kraken template * docs: updated some info * fix: updated igenomes_base path	2019-08-05 11:19:05 +02:00
Alexander Peltzer	82ffedf895	Drop aquila	2019-07-30 18:53:36 +02:00
Alexander Peltzer	4e48d4cc62	Fix remaining points by drpatelh	2019-07-30 18:53:00 +02:00
Alexander Peltzer	35c715ca3b	Merge remote-tracking branch 'upstream/master'	2019-07-30 16:53:19 +02:00
Remi Planel	1c0d596582	Merge remote-tracking branch 'upstream/master'	2019-07-30 16:15:20 +02:00
Remi Planel	be28a34839	Updat Pasteur doc	2019-07-30 16:12:30 +02:00
Remi Planel	64e78a3dc1	Update the doc	2019-07-30 15:17:25 +02:00
Remi Planel	6f264ac2ca	Add pasteur profile doc	2019-07-30 15:15:30 +02:00
marchoeppner	b74f020f14	Update docs/ccga_dx.md ... Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>	2019-07-29 12:45:30 +02:00
marchoeppner	71bc98afae	Adding config file for CCGA dx cluster	2019-07-29 12:06:29 +02:00
Olga Botvinnik	474e98daaf	Merge branch 'master' into olgabot/czb-update	2019-07-09 16:02:25 -07:00
marchoeppner	fe0153befd	Updating CCGA documentation	2019-07-05 08:30:02 +02:00
marchoeppner	d66bf4e478	Updating CCGA documentation	2019-07-05 08:28:18 +02:00
Olga Botvinnik	b82d68c009	Add docs	2019-06-24 17:55:01 -07:00
Alexander Peltzer	ebe838ac7e	Merge pull request #45 from czbiohub/olgabot/czbiohub ... [WIP] Add CZ Biohub	2019-06-06 13:35:34 +02:00
Olga Botvinnik	ad7e26ea69	Write out docs for czbiohub" ... git push	2019-06-05 14:42:24 -07:00
Alexander Peltzer	515e9484de	Merge pull request #44 from drpatelh/dev ... Add proper nf-core logo	2019-06-01 12:36:57 +02:00
drpatelh	ac804859f4	Add nf-core logo	2019-05-31 00:47:06 +01:00
Alexander Peltzer	0acdcc3813	Add Aquila Config Singapore	2019-05-04 23:20:15 +02:00
Tobias Schraink	d91b06d884	added missing line in prince and bigpurple docs	2019-04-18 14:25:27 -04:00
Tobias Schraink	4ba831705d	added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs	2019-04-18 14:13:02 -04:00
KochTobi	aaa7be049a	Update cfc config ... * Change singularity version documentation	2019-03-16 14:11:59 +01:00
James A. Fellows Yates	e503a3a064	Added new cluster and singularity cache	2019-03-14 21:21:31 +01:00
phue	13df59bfaf	remove singularity support ... reasons: * the kernel running on the compute nodes does not support overlayfs und thus containers downloaded from public registries won't run because they lack the /lustre mountpoint * building containers manually using the Singularity file would work, however nf-core pipelines will stop providing these files in future releases	2019-03-12 17:57:31 +00:00
phue	6fc65b54a2	add mendel.md	2019-02-27 22:26:31 +00:00
drpatelh	24fb466bc0	Changed description for Singularity image download	2019-01-11 14:52:15 +00:00
Harshil Patel	789d211b18	Update munin.md	2019-01-11 14:32:35 +00:00
Martin Proks	7acd9cf7df	Updating suggested changes	2019-01-11 15:28:10 +01:00
Martin Proks	89dbb6c061	Setting Singularity as default method	2019-01-11 14:37:12 +01:00
Martin Proks	548c8bca3f	Updated munin doc and configuration	2019-01-10 15:46:16 +01:00
James A. Fellows Yates	f62613588f	Removed newline typo	2019-01-07 20:35:40 +01:00
James A. Fellows Yates	2344b16693	Merge pull request #1 from jfy133/SHH_documentation ... Create shh documentation	2019-01-07 20:28:47 +01:00
James A. Fellows Yates	7f3acac4f4	Create shh documentation	2019-01-07 20:28:31 +01:00
James A. Fellows Yates	0325e556f2	Fixed the mysterious 'insert here' Institution	2019-01-07 20:25:39 +01:00
Phil Ewels	66a08891c7	Documentation tweaks	2019-01-07 14:25:06 +01:00
Phil Ewels	325dfe3968	Update docs/binac.md ... Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>	2019-01-07 12:11:31 +01:00
Phil Ewels	1758fbc11c	Update docs/cfc.md ... Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>	2019-01-07 12:11:19 +01:00
Phil Ewels	6d14461adc	Update docs/template.md ... Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>	2019-01-07 12:11:02 +01:00
Phil Ewels	94e546fd4b	Update docs/uzh.md ... Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>	2019-01-07 12:10:41 +01:00
Alexander Peltzer	02e97811c6	Get rid of template / iGenomes stuff	2019-01-07 11:21:17 +01:00
Alexander Peltzer	6a12e763ea	Get rid of examples	2019-01-07 11:16:58 +01:00
Alexander Peltzer	ce4b0373fa	Add in UZH	2019-01-06 15:35:26 +01:00
Alexander Peltzer	0d7ae3717f	Add in docs for CFC cluster	2019-01-06 15:34:52 +01:00
Alexander Peltzer	d5f41d837c	Remove non-required heading	2019-01-04 17:14:08 +01:00
Alexander Peltzer	c2fa8d5441	Add BINAC documentation	2019-01-04 17:13:03 +01:00
Alexander Peltzer	bcd85940fa	Add Template for Documentation of Cluster Resources	2019-01-04 17:12:59 +01:00
drpatelh	c58aaef190	Minor modifications	2018-11-29 17:49:19 +00:00
drpatelh	08dce7453a	Added bash statement to code-block	2018-11-29 15:12:35 +00:00
drpatelh	891d83b249	Fixed a type	2018-11-29 12:15:02 +00:00
drpatelh	fd226aac33	Properly changed link to crick.config	2018-11-28 17:04:33 +00:00
drpatelh	a2c848c8e4	Changed link to crick.config	2018-11-28 17:03:35 +00:00
drpatelh	c49ef07a1e	Changed link to reference genomes docs	2018-11-28 17:02:02 +00:00
drpatelh	64dd812fad	Bit of restructuring	2018-11-28 16:58:09 +00:00
drpatelh	0c598846e0	Modified README and added crick config	2018-11-27 09:17:55 +00:00